Locus 7244

Sequence ID 3L_DroMel_CAF1
Location 19,398,364 – 19,398,548
Length 184
Max. P 0.996731
window11773 window11774 window11775 window11776 window11777

overview

Window 3

Location 19,398,364 – 19,398,482
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 95.51
Mean single sequence MFE -27.90
Consensus MFE -25.72
Energy contribution -25.80
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.93
Structure conservation index 0.92
SVM decision value 2.74
SVM RNA-class probability 0.996731
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19398364 118 + 23771897
AGGUAAAGUUCAAUUAGCGCCAAUACUUUCCGAACUCUGCCACAAGCUGAUUUAAUUAAUAAGUUAUAAAAGGCACUCGGCGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGC
..................((((.......((((....((((......(((((((.....))))))).....)))).)))).((.((((((((((.......)))))))))).)))))) ( -28.40)
>DroSec_CAF1 37577 118 + 1
AGGUAAAGUUCAAUUGGCGCCAAUACUUUCCGAACUCUGCCACAAGCUGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGAUGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGC
.((.(((((...((((....))))))))))).......((((...(((....(((((....))))).....))).......((.((((((((((.......)))))))))).)))))) ( -28.50)
>DroSim_CAF1 37466 118 + 1
AGGUAAAGUUCAAUUAGCGCCAAUACUUUCCGAACUCUGCCACAAGCUGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGGCGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGC
..................((((.......((((....((((....(.(((((((.....))))))).)...)))).)))).((.((((((((((.......)))))))))).)))))) ( -28.40)
>DroEre_CAF1 32519 118 + 1
GGGUAAAGUUCAAUUAGCGCCAAUACUUUCCGAACUCUGCCACAAGCUGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGGCGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUUCU
.((((.(((((....((........))....))))).))))....(((....(((((....))))).....)))....((.((.((((((((((.......)))))))))).)).)). ( -27.50)
>DroYak_CAF1 63191 118 + 1
AGCUAAAGUUCAAUUAGGGCCAAUACUUUCCGAACUCUGCCACAAGCCGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGGCAAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUUUC
......(((((....((........))....))))).((((....(((....(((((....))))).....)))....))))..((((((((((.......))))))))))....... ( -26.70)
>consensus
AGGUAAAGUUCAAUUAGCGCCAAUACUUUCCGAACUCUGCCACAAGCUGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGGCGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGC
.((((.(((((....((........))....))))).))))....(((....(((((....))))).....))).......((.((((((((((.......)))))))))).)).... (-25.72 = -25.80 +   0.08)

alignment

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secondary structure

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Window 4

Location 19,398,364 – 19,398,482
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 95.51
Mean single sequence MFE -32.92
Consensus MFE -26.86
Energy contribution -27.34
Covariance contribution 0.48
Combinations/Pair 1.05
Mean z-score -2.04
Structure conservation index 0.82
SVM decision value 1.21
SVM RNA-class probability 0.931429
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19398364 118 - 23771897
GCCAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCGCCGAGUGCCUUUUAUAACUUAUUAAUUAAAUCAGCUUGUGGCAGAGUUCGGAAAGUAUUGGCGCUAAUUGAACUUUACCU
((((((.((((((((((.(....))))))))))).))..(((((....((((............))))...)))))))))(((((((((..(((......)))..))))))))).... ( -32.30)
>DroSec_CAF1 37577 118 - 1
GCCAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCAUCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCAGCUUGUGGCAGAGUUCGGAAAGUAUUGGCGCCAAUUGAACUUUACCU
((((((.((((((((((.(....))))))))))).))..(((((...((((((.........))))))...)))))))))((((((((......((((....)))))))))))).... ( -32.70)
>DroSim_CAF1 37466 118 - 1
GCCAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCGCCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCAGCUUGUGGCAGAGUUCGGAAAGUAUUGGCGCUAAUUGAACUUUACCU
((((((.((((((((((.(....))))))))))).))..(((((...((((((.........))))))...)))))))))(((((((((..(((......)))..))))))))).... ( -34.10)
>DroEre_CAF1 32519 118 - 1
AGAAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCGCCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCAGCUUGUGGCAGAGUUCGGAAAGUAUUGGCGCUAAUUGAACUUUACCC
....((.((((((((((.(....))))))))))).))((((...((.((((((.........))))))...))...))))(((((((((..(((......)))..))))))))).... ( -31.00)
>DroYak_CAF1 63191 118 - 1
GAAAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUUGCCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCGGCUUGUGGCAGAGUUCGGAAAGUAUUGGCCCUAAUUGAACUUUAGCU
.((((..((((((((((((((.......((.((((((((((...(((((((((.........))))))..)))...)))))))))).))..))))))))))).)))....)))).... ( -34.50)
>consensus
GCCAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCGCCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCAGCUUGUGGCAGAGUUCGGAAAGUAUUGGCGCUAAUUGAACUUUACCU
....((.((((((((((.(....))))))))))).))((((...((.((((((.........))))))...))...))))(((((((((..(((......)))..))))))))).... (-26.86 = -27.34 +   0.48)

alignment

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secondary structure

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Window 5

Location 19,398,404 – 19,398,515
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 95.41
Mean single sequence MFE -30.07
Consensus MFE -25.86
Energy contribution -26.86
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -2.28
Structure conservation index 0.86
SVM decision value 2.53
SVM RNA-class probability 0.994979
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19398404 111 + 23771897
CACAAGCUGAUUUAAUUAAUAAGUUAUAAAAGGCACUCGGCGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGCCGGUGUAACAGCUGCGCACGGAUUAAAGCUCGU
.((.((((...((((((.....((........((((.((((((.((((((((((.......)))))))))).))..)))))))).......)).....)))))))))).)) ( -32.76)
>DroSec_CAF1 37617 111 + 1
CACAAGCUGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGAUGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGCCGGUGUAACAGCUGCGCAAGGAUUAAAGCUCGU
.((.((((...((((((.....((((.((..(((.(.....((.((((((((((.......)))))))))).)).))))..)))))).....(....))))))))))).)) ( -29.40)
>DroSim_CAF1 37506 111 + 1
CACAAGCUGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGGCGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGCCGGUGUAACAGCUGCGCAAGGAUUAAAGCUCGU
....(((((...(((((....)))))......((((.((((((.((((((((((.......)))))))))).))..))))))))..))))).(....)............. ( -32.80)
>DroEre_CAF1 32559 111 + 1
CACAAGCUGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGGCGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUUCUCGGUGUAACAGCUGCGCAAAGAUUAAAGCUCGU
.....(((....(((((....))))).....)))...((((((.((((((((((.......)))))))))).)).(((..(((((.....)))))..))).....)).)). ( -27.20)
>DroYak_CAF1 63231 111 + 1
CACAAGCCGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGGCAAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUUUCCGUUGUAACAGCUGCGCAAAGAUUAAAGCUCGU
.....(((....(((((....))))).....)))...((((...((((((((((.......))))))))))((((((.(((.((....)).))).))))))....)).)). ( -28.20)
>consensus
CACAAGCUGAUUUAAUUAAUAAGUUAUCAAAGGCACUCGGCGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGCCGGUGUAACAGCUGCGCAAGGAUUAAAGCUCGU
.((.((((...((((((.....((........((((.((((((.((((((((((.......)))))))))).))..)))))))).......)).....)))))))))).)) (-25.86 = -26.86 +   1.00)

alignment

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secondary structure

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Window 6

Location 19,398,404 – 19,398,515
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 95.41
Mean single sequence MFE -29.17
Consensus MFE -26.86
Energy contribution -27.34
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.92
SVM decision value 1.81
SVM RNA-class probability 0.978071
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19398404 111 - 23771897
ACGAGCUUUAAUCCGUGCGCAGCUGUUACACCGGCCAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCGCCGAGUGCCUUUUAUAACUUAUUAAUUAAAUCAGCUUGUG
((((((((((((..(((...........(((((((..((.((((((((((.(....))))))))))).)))))).)))............)))..)))))...))))))). ( -30.30)
>DroSec_CAF1 37617 111 - 1
ACGAGCUUUAAUCCUUGCGCAGCUGUUACACCGGCCAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCAUCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCAGCUUGUG
(((((((.........((((.((((......))))..((.((((((((((.(....))))))))))).)).....))))..((((((...)))))).......))))))). ( -30.50)
>DroSim_CAF1 37506 111 - 1
ACGAGCUUUAAUCCUUGCGCAGCUGUUACACCGGCCAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCGCCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCAGCUUGUG
.((((........))))((((((((...(((((((..((.((((((((((.(....))))))))))).)))))).)))...((((((...))))))......)))).)))) ( -31.70)
>DroEre_CAF1 32559 111 - 1
ACGAGCUUUAAUCUUUGCGCAGCUGUUACACCGAGAAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCGCCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCAGCUUGUG
(((((((.............((.((((((((((....((.((((((((((.(....))))))))))).))..)).)))....))))).)).............))))))). ( -25.67)
>DroYak_CAF1 63231 111 - 1
ACGAGCUUUAAUCUUUGCGCAGCUGUUACAACGGAAAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUUGCCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCGGCUUGUG
(((((((.........((((.(......)..(((...((.((((((((((.(....))))))))))).)).))).))))..((((((...)))))).......))))))). ( -27.70)
>consensus
ACGAGCUUUAAUCCUUGCGCAGCUGUUACACCGGCCAGAUAUUGGGUUAAUGCUGGCUUAACCCAAUUUCGCCGAGUGCCUUUGAUAACUUAUUAAUUAAAUCAGCUUGUG
(((((((.........((((.((((......))))..((.((((((((((.(....))))))))))).)).....))))..((((((...)))))).......))))))). (-26.86 = -27.34 +   0.48)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,398,444 – 19,398,548
Length 104
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 82.71
Mean single sequence MFE -31.37
Consensus MFE -16.76
Energy contribution -20.85
Covariance contribution 4.09
Combinations/Pair 1.08
Mean z-score -3.22
Structure conservation index 0.53
SVM decision value 0.56
SVM RNA-class probability 0.782237
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19398444 104 + 23771897
CGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGCCGGUGUAACAGCUGCGCACGGAUUAAAGCUCGU-------UAAGAAGGUGACUUCCGAGUUUCC------UAUCAAAUC
.((.((((((((((.......)))))))))).)).((((((((((.....))))).)))....(((((((.-------...((((....)))))))))))))------......... ( -35.00)
>DroSec_CAF1 37657 104 + 1
UGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGCCGGUGUAACAGCUGCGCAAGGAUUAAAGCUCGU-------UAAGAAGGUGACUUCCGAGUUUCC------UAUCAAAUC
.((.((((((((((.......)))))))))).))..((((((......)))).)).((((....((((((.-------...((((....)))))))))))))------)........ ( -34.40)
>DroSim_CAF1 37546 104 + 1
CGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGCCGGUGUAACAGCUGCGCAAGGAUUAAAGCUCGU-------UAAGAAGGUGACUUCCGAGUUUCC------UAUCAAAUC
.((.((((((((((.......)))))))))).))..((((((......)))).)).((((....((((((.-------...((((....)))))))))))))------)........ ( -34.70)
>DroEre_CAF1 32599 104 + 1
CGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUUCUCGGUGUAACAGCUGCGCAAAGAUUAAAGCUCGU-------UAAGAAGGUGACUUCCGAGUUUCC------UAUCAAAUC
.((.((((((((((.......)))))))))).)).(((..(((((.....)))))..)))...(((((((.-------...((((....)))))))))))..------......... ( -32.30)
>DroYak_CAF1 63271 104 + 1
CAAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUUUCCGUUGUAACAGCUGCGCAAAGAUUAAAGCUCGU-------UAAGAAGGUGACUUCCGAGUUUCC------UAUCAAAUC
....((((((((((.......))))))))))((((((.(((.((....)).))).))))))..(((((((.-------...((((....)))))))))))..------......... ( -31.40)
>DroAna_CAF1 35492 112 + 1
--AAAGUGGGUUAAUCUAGCAUUAACCCCAUUUCCCCACAAUGCAA---CUGCGAAAGUAUAAAAGUUUAUGAAACCUUAAAGUGGAAAAUGCCAAUUCCCCAACUUAAAUCAAAUC
--.((((((((((((.....))))))))(((((..((((.......---.(((....)))......((((........)))))))).)))))...........)))).......... ( -20.40)
>consensus
CGAAAUUGGGUUAAGCCAGCAUUAACCCAAUAUCUGGCCGGUGUAACAGCUGCGCAAGGAUUAAAGCUCGU_______UAAGAAGGUGACUUCCGAGUUUCC______UAUCAAAUC
....((((((((((.......)))))))))).........(((((.....)))))........(((((((...........((((....)))))))))))................. (-16.76 = -20.85 +   4.09)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:00 2006